Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A3 F2 I1 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA Exported 232,901 C→T 58.7% intergenic (‑140/+30) hemB ← / ← ykiB porphobilinogen synthase/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*Exported232,9010CT58.7% 29.3 / 67.8 63intergenic (‑140/+30)hemB/ykiBporphobilinogen synthase/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (7/19);  new base T (14/23);  total (21/42)
Fisher's exact test for biased strand distribution p-value = 4.24e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.46e-01

GCGATGTTGACAAGAAGAGAATGGAAGAGAGGCCAGGACATCTTTTTAATAGAAACAGCAATAACTTTATATTCACTGAAAATATTTTTAATCTTTATTTATAGCTGTTGGTTATTATTTTTTGGAGTTTGG  >  Exported/232837‑232968
                                                                |                                                                   
gcgATGTTGACAAGAAGAGAATGGAAGAGAGGCCAGGACATCTTTTTAATAGAAACAGCAATAATTTtata                                                               <  1:2929584/71‑1 (MQ=255)
  gATGTTGACAAGAAGAGAATGGAAGAGAGGCCAGGACATCTTTTTAATAGAAACAGCAATAATTTTATAtt                                                             <  1:2139062/71‑1 (MQ=255)
  gATGTTGACAAGAAGAGAATGGAAGAGAGGCCAGGACATCTTTTTAATAGAAACAGCAATAACTTTATAtt                                                             <  1:5074305/71‑1 (MQ=255)
   aTGTTGACAAGAAGAGAATGGAAGAGAGGCCAGGACATCTTTTTAATAGAAACAGCAATAATTTTATAtt                                                             >  1:2662273/1‑70 (MQ=255)
    tGTTGACAAGAAGAGAATGGAAGAGAGGCCAGGACATCTTTTTAATAGAAACAGCAATAATTTTATATTCa                                                           >  1:2468873/1‑71 (MQ=255)
         aCAAGAAGAGAATGGAAGAGAGGCCAGGACATCTTTTTAATAGAAACAGCAATAATTTTATATTc                                                            <  1:2832149/65‑1 (MQ=255)
            agaagaGAATGGAAGAGAGGCCAGGACATCTTTTTAATAGAAACAGCAATAATTTTATATTCACTGaaaa                                                    >  1:3900960/1‑70 (MQ=255)
            agaagaGAATGGAAGAGAGGCCAGGACATCTTTTTAATAGAAACAGCAATAACTTTatat                                                              <  1:4767454/60‑1 (MQ=255)
              aagaGAATGGAAGAGAGGCCAGGACATCTTTTTAATAGAAACAGCAATAACTTTATATTc                                                            >  1:4871433/1‑60 (MQ=255)
               agagAATGGAAGAGAGGCCAGGACATCTTTTTAATAGAAACAGCAATAATTTTATATTCACTGAAAatat                                                 <  1:5641685/70‑1 (MQ=255)
                gagaATGGAAGAGAGGCCAGGACATCTTTTTAATAGAAACAGCAATAACTTTATATTCACTGAAAATAttt                                               <  1:5615426/71‑1 (MQ=255)
                gagaATGGAAGAGAGGCCAGGACATCTTTTTAATAGAAACAGCAATAACTTTATATTCACTGAAAATAttt                                               <  1:256780/71‑1 (MQ=255)
                  gaATGGAAGAGAGGCCAGGACATCTTTTTAATAGAAACAGCAATAATTTTATATTc                                                            >  1:5427913/1‑56 (MQ=255)
                   aaTGGAAGAGAGGCCAGGACATCTTTTTAATAGAAACAGCAATAATTTTATATTCACTGAAAATATTTTTa                                            <  1:3284849/71‑1 (MQ=255)
                   aaTGGAAGAGAGGCCAGGACATCTTTTTAATAGAAACAGCAATAACttt                                                                  <  1:397576/49‑1 (MQ=255)
                   aaTGGAAGAGAGGCCAGGACATCTTTTTAATAGAAACAGCAATAACTTTATATTCACTGAAAATAttttt                                             >  1:524096/1‑70 (MQ=255)
                       gAAGAGAGGCCAGGACATCTTTTTAATAGAAACAGCAATAATTTTATATTCACTGAAAATATTTTTAATCt                                        >  1:3759149/1‑71 (MQ=255)
                        aaGAGAGGCCAGGACATCTTTTTAATAGAAACAGCAATAATTTTATATTCACTGAAAATATTTTTa                                            <  1:2242839/66‑1 (MQ=255)
                            gagGCCAGGACATCTTTTTAATAGAAACAGCAATAATTTtat                                                                >  1:450990/1‑42 (MQ=255)
                            gagGCCAGGACATCTTTTTAATAGAAACAGCAATAATTTTATAtt                                                             >  1:5470276/1‑45 (MQ=255)
                            gagGCCAGGACATCTTTTTAATAGAAACAGCAATAATTTTATAtt                                                             >  1:2429901/1‑45 (MQ=255)
                             agGCCAGGACATCTTTTTAATAGAAACAGCAATAATTTTATATTCACTGAAAATATTTTTAATCtttattt                                  <  1:5184751/71‑1 (MQ=255)
                             agGCCAGGACATCTTTTTAATAGAAACAGCAATAATTTTATATTCACTGAAAATATTTTTAATCtttatt                                   <  1:1035991/70‑1 (MQ=255)
                               gCCAGGACATCTTTTTAATAGAAACAGCAATAATTTTATATTCACTGAAAATATTTTTAATCTttatttat                                <  1:5639625/71‑1 (MQ=255)
                                    gACATCTTTTTAATAGAAACAGCAATAACTTTATATTCACTGAAAATATTTTTa                                            <  1:4693547/54‑1 (MQ=255)
                                      cATCTTTTTAATAGAAACAGCAATAACTTTATATTCACTGAAAata                                                  >  1:1007049/1‑46 (MQ=255)
                                      cATCTTTTTAATAGAAACAGCAATAACTTTATATTCACTGAAAata                                                  >  1:1031448/1‑46 (MQ=255)
                                      cATCTTTTTAATAGAAACAGCAATAACTTTATATTCACTGAAAATATTTTTAATCTTTATTTATAGCTGtt                         >  1:839019/1‑71 (MQ=255)
                                       aTCTTTTTAATAGAAACAGCAATAATTTTATATTCACTGAAAATATTTTTAATCtttat                                    <  1:3496616/59‑1 (MQ=255)
                                          tttttAATAGAAACAGCAATAATTTTATATTCACTGAAAATAttt                                               >  1:3919040/1‑45 (MQ=255)
                                          tttttAATAGAAACAGCAATAATTTTATATTCACTGAAAATATTTTTAATCtttatt                                   <  1:2958326/57‑1 (MQ=255)
                                          tttttAATAGAAACAGCAATAATTTTATATTCACTGAAAATATTTTTAATCTTTATTTATAGCTGTTGGt                      >  1:5231601/1‑70 (MQ=255)
                                          tttttAATAGAAACAGCAATAACTTTATATTCACTGAAAATATTTTTAATCTTTATTTATAGc                             <  1:3134472/63‑1 (MQ=255)
                                          tttttAATAGAAACAGCAATAACTTTATATTCACTGAAAATATTTTTAATCTTTATTTATAGc                             <  1:3459387/63‑1 (MQ=255)
                                          tttttAATAGAAACAGCAATAACTTTATATTCACTGAAAATATTTTTAATCTTTATTTATAGc                             <  1:191558/63‑1 (MQ=255)
                                            tttAATAGAAACAGCAATAATTTTATATTCACTGAAAATATTTTTAATCtttatt                                   <  1:697747/55‑1 (MQ=255)
                                            tttAATAGAAACAGCAATAATTTTATATTCACTGAAAATATTTTTAATCtttat                                    >  1:5137880/1‑54 (MQ=255)
                                            tttAATAGAAACAGCAATAATTTTATATTCACTGAAAATATTTTTAATCTTTATTTATAGCTGTTGGt                      <  1:2524299/68‑1 (MQ=255)
                                            tttAATAGAAACAGCAATAACTTTATATTCACTGAAAATATTTTTAATCt                                        >  1:2148306/1‑50 (MQ=255)
                                                 tAGAAACAGCAATAATTTTATATTCACTGAAAATATTTTTAATCtttatt                                   <  1:4123630/50‑1 (MQ=255)
                                                 tAGAAACAGCAATAATTTTATATTCACTGAAAATATTTTTAATCTTTATTTATAGCTGTTGGTTATTAttt              <  1:4339360/71‑1 (MQ=255)
                                                 tAGAAACAGCAATAATTTTATATTCACTGAAAATATTTTTAATCTTTATTTATAGCTGTTGGTTATTAttt              >  1:2586505/1‑71 (MQ=255)
                                                 tAGAAACAGCAATAACTTTATATTCACTGAAAATATTTTTAATCtttat                                    <  1:1021017/49‑1 (MQ=255)
                                                 tAGAAACAGCAATAACTTTATATTCACTGAAAATATTTTTAATCtttat                                    <  1:3421625/49‑1 (MQ=255)
                                                  aGAAACAGCAATAACTTTATATTCACTGAAAATATTTTTAATCtttat                                    <  1:554990/48‑1 (MQ=255)
                                                   gAAACAGCAATAATTTTATATTCACTGAAAATATTTTTAATCTTTATTTATAGCTGTTGGTTATTAtttt             <  1:2371485/70‑1 (MQ=255)
                                                   gAAACAGCAATAACTTTATATTCACTGAAAATATTTTTAATCTTTATTTATAGCTGTTGGTTATTAttttt            <  1:402528/71‑1 (MQ=255)
                                                   gAAACAGCAATAACTTTATATTCACTGAAAATATTTTTAATCTTTATTTATAGCTGTTGGTTATTAttttt            <  1:395982/71‑1 (MQ=255)
                                                   gAAACAGCAATAACTTTATATTCACTGAAAATATTTTTAATCTTTATTTATAGCTGTTGGTTATTAtttt             <  1:2591260/70‑1 (MQ=255)
                                                    aaaCAGCAATAATTTTATTTTCACTGAAAATATTTTTAATCttta                                     <  1:2596045/45‑1 (MQ=38)
                                                    aaaCAGCAATAATTTTATATTCACTGAAAATATTTTTAATCtttat                                    <  1:3956401/46‑1 (MQ=255)
                                                    aaaCAGCAATAATTTTATAATCACTGAAAATATTTTTAATCttta                                     <  1:90607/45‑1 (MQ=38)
                                                     aaCAGCAATAATTTTATATTCACTGAAAATATTTTTAATCTTTATTTATAGCTGTTGGTTATTATTTTTTg          <  1:2625964/71‑1 (MQ=255)
                                                     aaCAGCAATAACTTTATATTCACTGAAAATATTTTTAATCTTTATTTATAGCt                            >  1:249193/1‑53 (MQ=255)
                                                      aCAGCAATAATTTTATATTCACTGAAAATATTTTTAATCtttatt                                   >  1:3918499/1‑45 (MQ=255)
                                                      aCAGCAATAATTTTATATTCACTGAAAATATTTTTAATCtttatt                                   >  1:3766119/1‑45 (MQ=255)
                                                      aCAGCAATAACTTTATATTCACTGAAAATATTTTTAATCTTTATTTATAGc                             <  1:804284/51‑1 (MQ=255)
                                                         gCAATAATTTTATATTCACTGAAAATATTTTTAATCTTTATTTATAGCTGTTGGTTATTATTTTTTGGAGt      <  1:4819461/71‑1 (MQ=255)
                                                          cAATAATTTTATATTCACTGAAAATATTTTTAATCTTTATTTATAGCTGTTGGTTATTATTTTTTGGAGtt     <  1:2705373/71‑1 (MQ=255)
                                                           aataatTTTATATTCACTGAAAATATTTTTAATCTTTATTTATAGCTGTTGGTTATTATTTTTTGGAGttt    <  1:5356455/71‑1 (MQ=255)
                                                             tAATTTTATATTCACTGAAAATATTTTTAATCTTTATTTATAGCTGTTGGTTATTATTTTTTGGAGTTTgg  <  1:1120363/71‑1 (MQ=255)
                                                             tAACTTTATATTCACTGAAAATATTTTTAATCttt                                      <  1:502377/35‑1 (MQ=255)
                                                             tAACTTTATATTCACTGAAAATATTTTTAATCttt                                      <  1:3099125/35‑1 (MQ=255)
                                                             tAACTTTATATTCACTGAAAATATTTTTAATCttt                                      <  1:2406958/35‑1 (MQ=255)
                                                                |                                                                   
GCGATGTTGACAAGAAGAGAATGGAAGAGAGGCCAGGACATCTTTTTAATAGAAACAGCAATAACTTTATATTCACTGAAAATATTTTTAATCTTTATTTATAGCTGTTGGTTATTATTTTTTGGAGTTTGG  >  Exported/232837‑232968

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A